Ok, so I got some work done today. I decided to take a look at the top end since TT mentioned the valves. Noticed a few things I might have overlooked in my hurry to get in and split the cases.
When I rebuilt the top end, I torqued all the bolts to the lower side of spec, but it might not have been tight enough after all (manual torque wrench). Looks like oil was getting into the chamber, though there were no leaks outside. Slick, oily residue that doesn't smell like gas in all chambers except 4 (which was running extra lean due to pilot jet blockage and upside down floats). Valve stem seals were all in place and accounted for, no oil on the valve stems beyond the seal, which is why I think torque wrench malfunction (user error).
In the process of removing the valves, I checked the exhaust valves first, replaced them, then started on the intake. When I flipped it over I accidentally pulled out the #2 exhaust again, and this time it stuck really bad on the way out, wouldn't go back in without a fight so I didn't make it. Not sure if it's galled on the end of the stem, or if I bent it when I reinstalled it, but it did NOT want to go back in. Removed all the valves again and checked that all were good and seated. Tested the other exhaust valves in valve guide #2's place to make sure it hadn't gouged the inside, and they felt smooth. So now I know I need to replace #2 exhaust valve - don't remember it being like that the first time, but I might have overlooked it.
Took a look at the pistons and noticed a hell of a lot more scoring on the skirts than I remembered during my previous rebuild. I didn't measure their width, nor the bore (no tools), but I ordered digital calipers and will check those. But judging by the scoring on the skirts and the jugs, it almost looks as if the pistons were bouncing around in their respective cylinders - scoring is evident in each cylinder, more prominently on the intake and exhaust sides of each bore, though there is some on each side. Not sure if this is what it looks like for the rings to seat, but this is how it looks. Fingernails don't catch, but you can see and feel that they are there. Lastly, there seems to be a little black splotch on the skirt of each piston on the intake side (visible in some photos). I don't know what that would indicate, but it doesn't wipe away very easily.
I also checked the the clearances of the sides of the piston rods to crank shaft. I could jostle the arms back and forth a bit (enough to make noise), but could not get a .35mm feeler all the way to the crank. It would stop on some part just above where the bearing meets the crank, so while it was technically between it, it wasn't on the shaft of the crank so I think it's ok (Clymer's wasn't very clear on this one).
And finally I made a video of the tranny countershaft bearing. You can see the rust starting to form on it, and you can hear the rattle it makes even when turning and jostling at low speeds when spun manually. But like I said before - this connects to the drive sprocket, and would not be turning or moving at all in idle at neutral, correct? Regardless, I think it might need replacing.
http://youtu.be/xOc173oPysINow with all this in conjunction with that rough sounding idle...what else should I be looking for? I still feel like there is something I'm missing deeper in the case.
